Sonny Software

Thanks for reading this Jon:
I am a long-time EndNote user, and I have written custom programs to address its missing features features when I need PubMed. I have repeatedly considered switching to Bookends since I also use Mellel but have not been able to convert due to workflow inefficiencies.
I would appreciate your response to these questions:

First:
EndNote uses MySQL as its embedded database engine. Its performance although stable, significantly deteriorates once libraries hit 5-digit number of citations and PDF attachments, especially when using non-SSD hard drives. How would Bookends handle such mega libraries?

Second:
Can Bookends import EndNote libraries and associated PDF attachments? Not a show-stopper but would certainly be useful to my case.

Third:
PubMed unfortunately has incorrect DOI for some of its citations. So when I import PDFs that are not automatically recognized and select "Autocomplete Paper..." from the contextual (right-click) menu, I am presented with the online search dialog that is autofilled with the DOI.
I would hope you agree a few tweaks would go a long way for some of your users:
1. A button to clear the search fields (e.g. would be faster then selecting all text in the DOI field and then deleting).
2. When text in the PDF pane is highlighted, it would be nice to have an option to transfer the highlighted text to the different search fields using the contextual right-click menu. It would also be great if the highlighted text could be simply dragged and dropped on the text fields of the above pane.
3. It would be nice if the search fields such as Journal and Year could optionally be persisted between repeated invocations of "Autocomplete Paper..."

Fourth:
My last suggestion pertains to PDF attachment display. Most monitors are rectangular. Side-by-side display of PDFs makes better use of the screen real estate than showing them below the list of references.
When selecting Attachments* from the "Main/Additional Fields/Notes/Attachments*" selections, I could not find a way to set the default zoom. If there is no way to set this globally, I think a setting in golbal preferences is needed. If I missed the setting, then I apologize. If there is no plan to implement such a feature, then I would suggest setting "Automatically Resize" as the selected default.

All the best and thank you in advance,


Navid

1. Bookends uses Valentina, which runs rings around MySQL.

https://valentina-db.com/en/

Note that there are other bottlenecks, though, such as some UI elements. My general advice is that you can handle 20-30K references easily. Above that you may notice some sluggishness.Although I know of one user with about 70K references, I wouldn't go above 50-60K myself in a single database. Of course you can have multiple smaller databases.

PDFs are stored on the HD, not in the database, so they don't affect speed *unless* you have many, many thousands. Since Bookends doesn't store direct links, but names, search speed can be affects. Again, we have users with 10;s of thousands of PDF with no issues. But be aware.

2, Please see this web page

https://www.sonnysoftware.com/bookends/ ... mport.html

3. (a) Maybe. You can click in the DOI field, Command-A, then delete. It doesn't happen often and isn't a big deal. More buttons = UI clutter.
(b) You can do that with the action popup menu at the top left now. You can't drag and drop (PDFKit controls that), but you can copy/paste.
(c) It would be rare that you would search for a PDF, click Import or Cancel or whatever, and independently do a search for the same one again. So the user would have to clear the fields each time (via a button or not), which would be quite annoying.

4. Automatically Resize is the default. You can change the zoom (via the popup or a right-click) and Bookends should remember when switching away and back to a PDF. This memory was added in a recent update.

Jon
Sonny Software

Thank you for your response. I am now officially a registered customer. I know of the Valentina engine but have never used it (only used SQLite as embedded engine). I often download my subscribed journals, annotate them and save them in a batch. Hence the request for persistence option of fields, but I see your point of view.
I had missed the top-left menu completely. Pity PDF-kit will not allow drag and drop. If the top-left menu item options would be added to the contextual menu that shows when right-clicking on the PDF display itself, the work-flow could be sped up. Is that a PDF-kit limitation too?
I now see that there are two ways of setting the zoom in the Attachments* pane. The one from the cog-wheel button persists. Thank you again.

At the end of this post is a list of PubMed stop words (https://www.ncbi.nlm.nih.gov/books/NBK3 ... stopwords/) that when included, cause PubMed title searches to fail.
E.g. search for the title below (in the "Autocomplete Paper..." dialog):
"Colonic Perforation After Computed Tomographic Colonography in a Patient with Fibrostenosing Crohn’s Disease"
and you get nothing. Now removing the words "in" and "a" as in the next prargraph and searching again finds the article (despite not removing "with," another stop word, PubMed certainly has inconsistencies):
"Colonic Perforation After Computed Tomographic Colonography Patient with Fibrostenosing Crohn’s Disease"
Any possibility to assist filtering these stop-words out for the PubMed title text search? E.g. another menu sub-item in the top left to add "PubMed-filtered text" or a better option that you could imagine?

Thanks again,
Navid

<STOPWORDS>
a, about, again, all, almost, also, although, always, among, an, and, another, any, are, as, at
be, because, been, before, being, between, both, but, by
can, could
did, do, does, done, due, during
each, either, enough, especially, etc
for, found, from, further
had, has, have, having, here, how, however
i, if, in, into, is, it, its, itself
just
kg, km
made, mainly, make, may, mg, might, ml, mm, most, mostly, must
nearly, neither, no, nor, not
obtained, of, often, on, or, our, overall
perhaps, pmid
quite
rather, really, regarding
seem, seen, several, should, show, showed, shown, shows, significantly, since, so, some, such
than, that, the, their, theirs, them, then, there, therefore, these, they, this, those, through, thus, to
upon, use, used, using
various, very
was, we, were, what, when, which, while, will, with, within, without, would
</STOPWORDS>

The stop words are words that PubMed filters out itself:

https://www.ncbi.nlm.nih.gov/books/NBK3 ... ing_PubMed

"PubMed breaks apart the phrase and repeats the above automatic term mapping process until a match is found. PubMed ignores stopwords in searches."

I've seen no documentation that users must do this themselves (why would they need to if PubMed is going to ignore them). I've played with removing some words automatically in the past and have found inconsistent results (some searches now work, some searches now fail). If you have seen any documentation that says how queries *should* remove stop words, please point me to it.

Jon
Sonny Software